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PathCase-SB architecture and database design
BACKGROUND: Integration of metabolic pathways resources and regulatory metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation in metabolic networks. Therefore, the tasks...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3229461/ https://www.ncbi.nlm.nih.gov/pubmed/22070889 http://dx.doi.org/10.1186/1752-0509-5-188 |
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author | Cakmak, Ali Qi, Xinjian Coskun, Sarp A Das, Mitali Cheng, En Cicek, A Ercument Lai, Nicola Ozsoyoglu, Gultekin Ozsoyoglu, Z Meral |
author_facet | Cakmak, Ali Qi, Xinjian Coskun, Sarp A Das, Mitali Cheng, En Cicek, A Ercument Lai, Nicola Ozsoyoglu, Gultekin Ozsoyoglu, Z Meral |
author_sort | Cakmak, Ali |
collection | PubMed |
description | BACKGROUND: Integration of metabolic pathways resources and regulatory metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation in metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks. DESCRIPTION: PathCase Systems Biology (PathCase-SB) is built and released. The PathCase-SB database provides data and API for multiple user interfaces and software tools. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate data of selected biological data sources on the web (currently, BioModels database and KEGG), and to provide more powerful and/or new capabilities via the new web-based integrative framework. This paper describes architecture and database design issues encountered in PathCase-SB's design and implementation, and presents the current design of PathCase-SB's architecture and database. CONCLUSIONS: PathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (real-time) access to the data in the database. PathCase-SB itself is already being used by researchers across the world. |
format | Online Article Text |
id | pubmed-3229461 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-32294612011-12-03 PathCase-SB architecture and database design Cakmak, Ali Qi, Xinjian Coskun, Sarp A Das, Mitali Cheng, En Cicek, A Ercument Lai, Nicola Ozsoyoglu, Gultekin Ozsoyoglu, Z Meral BMC Syst Biol Database BACKGROUND: Integration of metabolic pathways resources and regulatory metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation in metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks. DESCRIPTION: PathCase Systems Biology (PathCase-SB) is built and released. The PathCase-SB database provides data and API for multiple user interfaces and software tools. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate data of selected biological data sources on the web (currently, BioModels database and KEGG), and to provide more powerful and/or new capabilities via the new web-based integrative framework. This paper describes architecture and database design issues encountered in PathCase-SB's design and implementation, and presents the current design of PathCase-SB's architecture and database. CONCLUSIONS: PathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (real-time) access to the data in the database. PathCase-SB itself is already being used by researchers across the world. BioMed Central 2011-11-09 /pmc/articles/PMC3229461/ /pubmed/22070889 http://dx.doi.org/10.1186/1752-0509-5-188 Text en Copyright ©2011 Cakmak et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Database Cakmak, Ali Qi, Xinjian Coskun, Sarp A Das, Mitali Cheng, En Cicek, A Ercument Lai, Nicola Ozsoyoglu, Gultekin Ozsoyoglu, Z Meral PathCase-SB architecture and database design |
title | PathCase-SB architecture and database design |
title_full | PathCase-SB architecture and database design |
title_fullStr | PathCase-SB architecture and database design |
title_full_unstemmed | PathCase-SB architecture and database design |
title_short | PathCase-SB architecture and database design |
title_sort | pathcase-sb architecture and database design |
topic | Database |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3229461/ https://www.ncbi.nlm.nih.gov/pubmed/22070889 http://dx.doi.org/10.1186/1752-0509-5-188 |
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